# Package picard.illumina

package picard.illumina

Related Packages
Package
Description
picard
picard.illumina.parser
picard.illumina.quality
Class
Description
BarcodeExtractor
BarcodeExtractor is used to match barcodes and collect barcode match metrics.
BarcodeExtractor.BarcodeMatch
Utility class to hang onto data about the best match for a given barcode
BarcodeMetric
Metrics produced by the ExtractIlluminaBarcodes program that is used to parse data in the basecalls directory and determine to which barcode each read should be assigned.
BasecallsConverter<CLUSTER_OUTPUT_RECORD>
BasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).
BasecallsConverter.ClusterDataConverter<OUTPUT_RECORD>
Interface that defines a converter that takes ClusterData and returns OUTPUT_RECORD type objects.
BasecallsConverter.ConvertedClusterDataWriter<OUTPUT_RECORD>
Interface that defines a writer that will write out OUTPUT_RECORD type objects.
BasecallsConverterBuilder<CLUSTER_OUTPUT_RECORD>
BasecallsConverterBuilder creates and configures BasecallsConverter objects.
CheckIlluminaDirectory
Program to check a lane of an Illumina output directory.
ClusterDataToSamConverter
Takes ClusterData provided by an IlluminaDataProvider into one or two SAMRecords, as appropriate, and optionally marking adapter sequence.
CollectIlluminaBasecallingMetrics
A Command line tool to collect Illumina Basecalling metrics for a sequencing run Requires a Lane and an input file of Barcodes to expect.
CollectIlluminaLaneMetrics
Command-line wrapper around `CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector`.
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
Utility for collating Tile records from the Illumina TileMetrics file into lane-level and phasing-level metrics.
DistanceMetric
ExtractBarcodesProgram
ExtractIlluminaBarcodes
Determine the barcode for each read in an Illumina lane.
ExtractIlluminaBarcodes.PerTileBarcodeExtractor
Extracts barcodes and accumulates metrics for an entire tile.
IlluminaBasecallingMetrics
Metric for Illumina Basecalling that stores means and standard deviations on a per-barcode per-lane basis.
IlluminaBasecallsToFastq
IlluminaBasecallsToFastq.ReadNameFormat
Simple switch to control the read name format to emit.
IlluminaBasecallsToSam
IlluminaBasecallsToSam transforms a lane of Illumina data file formats (bcl, locs, clocs, qseqs, etc.) into SAM, BAM or CRAM file format.
IlluminaLaneMetrics
Embodies characteristics that describe a lane.
IlluminaPhasingMetrics
Metrics for Illumina Basecalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis.
LanePhasingMetricsCollector
Helper class used to transform tile data for a lane into a collection of IlluminaPhasingMetrics
MarkIlluminaAdapters
Command line program to mark the location of adapter sequences.
SortedBasecallsConverter<CLUSTER_OUTPUT_RECORD>
SortedBasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).
UnsortedBasecallsConverter<CLUSTER_OUTPUT_RECORD>
UnortedBasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).